Code
# load libraries
library(tidyverse)
library(here)
library(janitor)
library(patchwork)
library(tsibble)
library(feasts)
library(fable)
library(dplyr)ESM 244 Homework 2
Task 2: Willamette Falls Fish Passage Time Series Summary
1 Overview
This report includes population data on Coho, Jack Coho, and Steelhead fish collected daily at the Willamette Falls fish ladder between 2001-2010. The plots below illustrate both the seasonality of fish species migrating through Willamette Falls and the general trend in population size over the ten year period. Also included is a forecasting model used to predict Coho Salmon population from 2010-2025.
2 Data
U.S. Army Corps of Engineers, NWD and Chelan, Douglas and Grant County PUDs, Yakima Klickitat Fisheries Project, Colville Tribes Fish & Wildlife (OBMEP), Oregon Department of Fish & Wildlife, Washington Department of Fish & Wildlife. 2010. Columbia River DART Adult Passage Counts Graphic & Text. WFF-Willamette Falls [2001]. Columbia Basin Research. University of Washington School of Aquatic and Fishery Sciences. https://www.cbr.washington.edu/dart/query/adult_graph_text
Code
# load and clean data
fish_data <- read_csv(here('data', 'willamette_fish_passage.csv'))
fish_df <- fish_data %>%
clean_names() %>%
mutate(date = lubridate:: mdy(date)) %>%
select(date, coho, jack_coho, steelhead) %>%
replace_na(list(coho=0, jack_coho=0, steelhead=0))Code
# convert to time series
fish_ts <- fish_df %>%
as_tsibble(key = NULL,
index = date)3 Part 1: Original Time Series
- The time series below shows a steady increase in Coho individuals between 2001-2010, with population size surpassing 1000 individuals around 2010.
- Jack coho populations remained relatively constant, apart from a notable peak at about 400 individuals in 2009.
- Steelhead populations have a seasonal but persistent presence at the Willamette Falls fish ladder, whereas both Coho and Jack coho are only observed there during specific small windows of the year.
Code
# plot time series for each species
coho <- ggplot(fish_ts, aes(x = date)) +
geom_line(aes(y = coho)) +
theme_minimal() +
labs(x = " ",
y = "Coho")
jack <- ggplot(fish_ts, aes(x = date)) +
geom_line(aes(y = jack_coho)) +
theme_minimal() +
labs(x = " ",
y = "Jack Coho")
steel <- ggplot(fish_ts, aes(x = date)) +
geom_line(aes(y=steelhead)) +
theme_minimal() +
labs(x = "Year",
y = "Steelhead")
fish_graph <- coho / jack / steel +
plot_annotation(title = "Fish Observed at the Willamette Falls Fish Ladder from 2001-2010" ,
caption = "The x axis represents time in years between 2001-2010. Note the difference in magnitude of the y axes; the top
graph showing population is measured for Coho salmon by intervals of 500, the middle graph showing population
trends for Jack Coho salmon increases by intervals of 50, and the bottom graph showing population trends for
Steelhead increases by intervals of 100.",
theme = theme(plot.title = element_text(size = 14, hjust = 0.5),
plot.caption = element_text(hjust = 0.5)))
fish_graph
4 Part 2: Seasonplots
- Coho and Jack coho are observed at the Willamette Falls fish ladder exclusively in and around October each year, whereas Steelhead are observed there year-round with peaks between mid spring to mid summer.
- The number of Coho individuals observed in the fall each year has increased between 2001-2010.
- Jack coho population appears to steadily rise to a peak in 2009 followed by population decline.
Code
# make individual time series for each fish species
coho_ts <- fish_df %>%
pivot_longer("coho":"steelhead",
names_to = "species",
values_to = "count") %>%
filter(species == "coho") %>%
as_tsibble(key = NULL,
index = date)
jack_ts <- fish_df %>%
pivot_longer("coho":"steelhead",
names_to = "species",
values_to = "count") %>%
filter(species == "jack_coho") %>%
as_tsibble(key = NULL,
index = date)
steel_ts <- fish_df %>%
pivot_longer("coho":"steelhead",
names_to = "species",
values_to = "count") %>%
filter(species == "steelhead") %>%
as_tsibble(key = NULL,
index = date)
# create season plots
coho_season <- coho_ts %>%
gg_season(y = count,
pal = rainbow(n=9)) +
theme_light() +
labs(x = " ",
y = "Coho") +
theme(legend.position = "none")
jack_season <- jack_ts %>%
gg_season(y = count,
pal = rainbow(n=9)) +
theme_light() +
labs(x = " ",
y = "Jack Coho")
steel_season <- steel_ts %>%
gg_season(y = count,
pal = rainbow(n=9)) +
theme_light() +
labs(x = "Year",
y = "Steelhead") +
theme(legend.position = "none")
fish_season <- coho_season / jack_season / steel_season +
plot_annotation(caption = "The plots above show the annual trends of fish species: coho (top), jack coho (center), and steelhead (bottom)
at the Willamette Falls fish ladder from 2001-2010. The x axis shows time in months and the y axes show counts of
individuals of each species. Note the different y-axes scales; Coho population is shown in intervals of 250,
Jack Coho in intervals of 50, and Steelhead 100. The colors represent each year between 2001-2010 with red representing
2001 followed by a rainbow gradient where purple and pink represent the most recent years. " ,
theme = theme(plot.caption = element_text(hjust = 0.5)))
fish_season
5 Part 3: Annual counts by species
- Note the different y-axis scales in each of the figures below. Coho populations reach a maximum of over 250,000 individuals; Steelhead about 50,000; and Jack coho only about 3,000 individuals.
- Coho salmon population levels were relatively low between 2001-2008 followed by a significant jump in 2009 followed by a slight decline in 2010.
- Jack coho populations experienced extreme fluctuations between 2001-2008. Whereas, steelhead populations appear relatively consistent if not slightly declining between 2001-2010.
Code
fish_totals <- fish_ts %>%
separate(date, c('year', 'month', 'day')) %>%
group_by(year) %>%
summarise(Coho = sum(coho),
Jack_Coho = sum(jack_coho),
Steelhead = sum(steelhead)) %>%
pivot_longer("Coho":"Steelhead",
names_to = "species",
values_to = "total")
fish_total_plot <- ggplot(data = fish_totals,
aes(x = year,
y = total,
fill = species)) +
geom_col() +
facet_wrap(~species, ncol=1, scales = "free") +
labs(x = "Year",
y = "Total Fish at Fish Ladder",
fill = "Fish Species",
caption = "The figures above show the annual totals for fish passage at the Willamette fish lader from 2001-2010.
The top graph (red) represents coho salmon, the center graph (green) represents jack coho salmon, and the
bottom graph (blue) represents steelhead. The x axis shows time in years, and the y axes represent number
of individuals for each species. Note the different y-axes scales for the different species; Coho population
is shown in intervals of 2500, Jack Coho in intervals of 500, and Steelhead 5000") +
theme(plot.caption = element_text(hjust = 0.5))
plot(fish_total_plot)
6 Optional: Forecast Salmon runs with Holt-Winters
Code
# create model
coho_month_df <- fish_df %>%
separate(date, c('year', 'month', 'day')) %>%
mutate(yearmonth = paste(year, month, sep = "-"),
date = yearmonth(yearmonth)) %>%
select(date, coho) %>%
group_by(date) %>%
summarise(count = sum(coho))
coho_month_ts <- coho_month_df %>%
as_tsibble(key = NULL,
index = date)
coho_fit <- coho_month_ts %>%
model(ets = ETS(count ~ season(method = "A") + trend(method = "A")))
coho_forecast <- coho_fit %>%
forecast(h = "15 years")
coho_forecast %>%
autoplot(coho_month_ts) 